*** empty log message ***

FilmGlsOptions.cc

@@ -107,9 +107,6 @@ void FilmGlsOptions::parse_command_line(int argc, char** argv, Log& logger)
     if ( arg == "-ms") {
       gopt->ms = atoi(argv[n+1]);
       n+=2;
-    } else if ( arg == "-sp" ) {
-      gopt->susanpath = argv[n+1];      
-      n+=2;
     } else if ( arg == "-rn" ) {
       gopt->datadir = argv[n+1];      
       n+=2;
@@ -154,7 +151,6 @@ void FilmGlsOptions::print_usage(int argc, char *argv[])
   cout << "Usage: " << argv[0] << " [options] <groupfile> [optional:<paradigmfile>] <thresh>\n\n"
        << "  Available options are:\n"
        << "        -sa                                (smooths auto corr estimates)\n"
-       << "        -sp <path>                         (susan path)\n"
        << "        -ms <num>                          (susan mask size)\n"
        << "        -epith <num>                       (set susan brightness threshold - otherwise it is estimated)\n"
        << "        -v                                 (outputs full data)\n"

FilmGlsOptions.h

@@ -30,7 +30,6 @@ class FilmGlsOptions {
   string paradigmfname;
   string epifname;
   string datadir;
-  string susanpath;
 
   string neffsfname;
   
@@ -79,7 +78,6 @@ inline FilmGlsOptions::FilmGlsOptions()
   // set up defaults
   neffsfname = "neffs";
   datadir = "results";
-  susanpath = "/usr/local/fsl/bin/susan_smooth";
   epifname = "epivolume";
   thresh = 0;
   inputfname = "";  

FilmGlsOptionsRes.cc

@@ -120,10 +120,6 @@ void FilmGlsOptionsRes::parse_command_line(int argc, char** argv, ofstream& logf
       gopt->ms = atoi(argv[n+1]);
       logfile << argv[n+1] << " ";
       n+=2;
-    } else if ( arg == "-sp" ) {
-      gopt->susanpath = argv[n+1];      
-      logfile << argv[n+1] << " ";
-      n+=2;
     } else if ( arg == "-iters") {
       gopt->numiters = atoi(argv[n+1]);
       logfile << argv[n+1] << " ";

FilmGlsOptionsRes.h

@@ -28,7 +28,6 @@ class FilmGlsOptionsRes {
   string contrastfname;
   string epifname;
   string datadir;
-  string susanpath;
 
   string neffsfname;
   string zscoresfname;
@@ -84,7 +83,6 @@ inline FilmGlsOptionsRes::FilmGlsOptionsRes()
   zscoresfname = "zstats";
   neffsfname = "neffs";
   datadir = "results";
-  susanpath = "/usr/local/fsl/bin/susan_smooth";
   epifname = "epivolume";
   thresh = 0;
   contrastfname = "";

FilmOlsOptions.cc

@@ -105,10 +105,6 @@ void FilmOlsOptions::parse_command_line(int argc, char** argv, ofstream& logfile
       gopt->ms = atoi(argv[n+1]);
       logfile << argv[n+1] << " ";
       n+=2;
-    } else if ( arg == "-sp" ) {
-      gopt->susanpath = argv[n+1];      
-      logfile << argv[n+1] << " ";
-      n+=2;
     } else if ( arg == "-rn" ) {
       gopt->datadir = argv[n+1];      
       logfile << argv[n+1] << " ";
@@ -150,8 +146,6 @@ void FilmOlsOptions::print_usage(int argc, char *argv[])
        << "        -det                               (detrend data as preprocessing step)\n"
        << "        -rn <dir>                          (directory name to store results in, default is "
        << gopt->datadir << ")\n"
-       << "        -sp <path>                         (path for SUSAN executable, default is "
-       << gopt->susanpath << ")\n"
        << "        -help\n\n";
 }
 

FilmOlsOptions.h

@@ -27,7 +27,6 @@ class FilmOlsOptions {
   string paradigmfname;
   string datadir;
   string epifname;
-  string susanpath;
 
   bool verbose;
   bool detrend;
@@ -71,7 +70,6 @@ inline FilmOlsOptions::FilmOlsOptions()
   epifname = "epivolume";
   inputfname = "";  
   paradigmfname = "";
-  susanpath = "/usr/local/fsl/bin/susan_smooth";
   
   thresh = 0;
   ms = 4;

film_gls_res.cc

@@ -143,7 +143,7 @@ int main(int argc, char *argv[])
 		    // Smooth raw estimates:
 		    if(globalopts.smoothACEst)
 		      {
-			acEst.spatiallySmooth(logger.getDir() + "/" + globalopts.epifname, epivol, globalopts.ms, globalopts.epifname, globalopts.susanpath, globalopts.epith);		    
+			acEst.spatiallySmooth(logger.getDir() + "/" + globalopts.epifname, epivol, globalopts.ms, globalopts.epifname, globalopts.epith);		    
 		      }
 		    if(globalopts.tukeysize == 0)
 		      globalopts.tukeysize = (int)(2*sqrt(sizeTS))/2;
@@ -159,7 +159,7 @@ int main(int argc, char *argv[])
 		    // Smooth raw estimates:
 		    if(globalopts.smoothACEst)
 		      { 
-			acEst.spatiallySmooth(logger.getDir() + "/" + globalopts.epifname, epivol, globalopts.ms, globalopts.epifname, globalopts.susanpath, globalopts.epith);		    
+			acEst.spatiallySmooth(logger.getDir() + "/" + globalopts.epifname, epivol, globalopts.ms, globalopts.epifname, globalopts.epith);		    
 		      }
 		
 		    acEst.pava();